Variant report

Variant	rs3846949
Chromosome Location	chr6:15371243-15371244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:15087474..15090425-chr6:15369909..15372876,2	K562	blood:
2	chr6:15366535..15368984-chr6:15370692..15373575,3	K562	blood:
3	chr6:15370293..15372055-chr6:15374139..15376123,3	K562	blood:
4	chr6:15371193..15373867-chr6:15377723..15380218,2	K562	blood:
5	chr6:15350348..15351999-chr6:15369721..15371306,2	MCF-7	breast:
6	chr6:15350037..15352732-chr6:15370116..15373857,3	K562	blood:
7	chr6:15367767..15369862-chr6:15371180..15373731,3	MCF-7	breast:
8	chr6:15365926..15369086-chr6:15370473..15372494,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234261	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10807584	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2072820	0.87[MKK][hapmap];0.93[YRI][hapmap]
rs2237160	0.87[MKK][hapmap];0.93[YRI][hapmap]
rs34338229	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6905698	0.82[MKK][hapmap];0.96[YRI][hapmap]
rs6924733	0.82[MKK][hapmap];0.93[YRI][hapmap]
rs9464786	0.86[MKK][hapmap];0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3846949	DEK	cis	cerebellum	SCAN
rs3846949	DEK	cis	parietal	SCAN
rs3846949	JARID2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15341800-15378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:15360400-15372400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:15360600-15371400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:15362200-15372200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:15362600-15372400	Enhancers	Fetal Lung	lung
7	chr6:15363000-15371600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:15364400-15372000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:15364600-15390200	Weak transcription	HepG2	liver
10	chr6:15365000-15402800	Weak transcription	Dnd41	blood
11	chr6:15365200-15371400	Weak transcription	Fetal Intestine Small	intestine
12	chr6:15365800-15372200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:15365800-15372400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr6:15365800-15374400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:15365800-15374400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr6:15365800-15378600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:15365800-15384800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:15366200-15372200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:15366400-15382600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:15366600-15372200	Enhancers	Brain Hippocampus Middle	brain
21	chr6:15366600-15372400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:15366600-15373600	Weak transcription	HSMMtube	muscle
23	chr6:15366600-15374400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:15366600-15375800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:15366600-15376000	Weak transcription	Osteobl	bone
26	chr6:15366600-15377200	Weak transcription	Stomach Mucosa	stomach
27	chr6:15366600-15378600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:15366600-15384800	Weak transcription	NH-A	brain
29	chr6:15366600-15385000	Weak transcription	Fetal Brain Female	brain
30	chr6:15366800-15372400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:15367000-15371400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:15367000-15373800	Weak transcription	HSMM	muscle
33	chr6:15367000-15375200	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:15367000-15376200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr6:15367000-15379200	Weak transcription	Brain Germinal Matrix	brain
36	chr6:15367000-15384800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr6:15367200-15375200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:15367400-15371600	Weak transcription	Fetal Intestine Large	intestine
39	chr6:15367400-15371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr6:15367400-15384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:15367400-15389400	Weak transcription	Ovary	ovary
42	chr6:15367600-15372200	Enhancers	Brain Anterior Caudate	brain
43	chr6:15367600-15372200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr6:15367600-15374200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr6:15367600-15374600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:15367800-15376000	Weak transcription	Liver	Liver
47	chr6:15368000-15372000	Enhancers	Brain Substantia Nigra	brain
48	chr6:15368200-15374200	Weak transcription	Small Intestine	intestine
49	chr6:15368200-15375200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:15368400-15374400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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